[gmx-users] Re: Structure preparation for the simulation

[James Starlight]

Itamar, thank you for advise but I dont like swith prot :))

Justin, what xleap prameter set have you used for KALP peptide? I want to
find parameters wich would not affect any problems in my further simulation
via gromos in Gromacs.


James



2011/10/31 Itamar Kass <itamar.kass at monash.edu>

> Hi James,
>
> I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html).
> Despite being an old and not well supported for any system, it is still a
> free and easy to use and allows the building and mutating of residues  in
> addition to automatically adding missing atoms.
>
> You can just build an extra GLY at the end of the your chain and using
> text editor change it to N/C-caps.
>
>
> Cheers,
> Itamar
>
> On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote:
>
> Dear Gromacs Users!
>
>
>
> I'd like to know about external software wich could be used for structure
>
> processing for the futher simulation in Gromacs. Today I've tried one of
> the
>
> most popular such software Amber tools but I've forced with problems during
>
> compilation of it ") So I'm looking for possible analogues )
>
>
> First of all I'm intresting in software for the addition different CAPing
>
> groups to N and C termi of my protein.
>
>
> Is there any plugins for Pymol or VMD for such purposes? I've loked for
> this
>
> option in both of that software but couldnot  find
>
>
>
> Thank you for your help,
>
>
> James
>
>
> Among free solutions... maybe this would help:
> http://www.chemaxon.com/marvin/sketch/index.php
>
> I don't know molecular editor plugins for VMD, but it would be cool,
> if one is accessible.
>
> --
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
> --
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> --
>
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail:  Itamar.Kass at monash.edu
> ============================================
>
>
>
>
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